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Efficient protocols for the extraction of microbial DNA from the rhizosphere of hydrophilic forests in Chile Ciencia e Investigación Agraria
Cáceres,Pablo; Cordero,Cecilia; González,Gloria; Quiroz,Karla; Bobadilla,Juan C; Bravo,Carmen; Caligari,Peter D.S; Carrasco,Basilio; García-Gonzales,Rolando.
A lysis buffer-based protocol (Protocol BA), a modified lysis buffer-based protocol (Protocol BA Mod) and a commercial extraction kit (Protocol PS Kit) (Power Soil, Mo bio Laboratories, CA USA) were each evaluated for their ability to produce high-quality DNA with yields sufficient to allow its use in biodiversity studies. Similarly, the effect of liquid nitrogen on the process of cell disruption in all of the protocols that were studied. DNA yields ranged from 12.4 ng g-1 of processed soil to 9620 ng g-1 using the modified lysis buffer and commercial extraction kit, respectively. The quality of the DNA was determined by the ability of the DNA to produce efficient and reproducible polymerase chain reaction (PCR) products, using primers for universal 16S...
Tipo: Journal article Palavras-chave: Hydrophilic forests; 16S ribosomal RNA; PCR; Rhizosphere; Soil DNA extraction.
Ano: 2012 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-16202012000300018
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Extraction of bulk DNA from Thar Desert soils for optimization of PCR-DGGE based microbial community analysis Electron. J. Biotechnol.
Kumar Gothwal,Raj; Kumar Nigam,Vinod; Mohan,M. Krishna; Sasmal,Dinakar; Ghosh,Purnendu.
A reliable method for characterizing microbial communities on the basis of their differences in the 16S ribosomal RNA (rRNA) gene sequences in the hot arid zone sandy soils has been optimized. A desert plant (Calligonum polygonoides) was chosen to provide the rhizospheric soil samples, collected from three different agro-ecological locations. Total community DNA was efficiently extracted at small-scale level using direct lysis with hot sodium dodecyl sulphate (SDS), glass bead beating and finally subjecting the sandy soil to liquid nitrogen freeze-thaw cycles. To amplify V3 region of bacterial 16S rRNA gene, universal conserved primers were used. Second round polymerase chain reaction (PCR) was attempted to increase product concentration and to minimize...
Tipo: Journal article Palavras-chave: Arid soils; Microbial community; PCR-DGGE; Rhizosphere; Soil DNA extraction.
Ano: 2007 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582007000300007
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